Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis
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Title
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis
Authors
Keywords
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Journal
Nature Communications
Volume 12, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2021-01-15
DOI
10.1038/s41467-020-20508-2
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Note: Only part of the references are listed.- Metabolomics with 15N Labeling for Characterizing Missing Monoterpene Indole Alkaloids in Plants
- (2020) Ryo Nakabayashi et al. ANALYTICAL CHEMISTRY
- Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy
- (2020) Qiushi Li et al. Nature Communications
- Building near-complete plant genomes
- (2020) Todd P Michael et al. CURRENT OPINION IN PLANT BIOLOGY
- Multiomics-based characterization of specialized metabolites biosynthesis in Cornus officinalis
- (2020) Amit Rai et al. DNA RESEARCH
- Evolution of new enzymes by gene duplication and divergence
- (2020) Shelley D. Copley FEBS Journal
- Higher dimensional metabolomics using stable isotope labeling for identifying the missing specialized metabolism in plants
- (2020) Ryo Nakabayashi et al. CURRENT OPINION IN PLANT BIOLOGY
- Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae
- (2020) Benjamin R Lichman et al. CURRENT OPINION IN PLANT BIOLOGY
- Active and repressed biosynthetic gene clusters have spatially distinct chromosome states
- (2020) Hans-Wilhelm Nützmann et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms
- (2019) Hiroshi Tsugawa et al. NATURE METHODS
- De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis
- (2019) Hideki Hirakawa et al. DNA RESEARCH
- Bifunctional Cytochrome P450 Enzymes Involved in Camptothecin Biosynthesis
- (2019) Yun Yang et al. ACS Chemical Biology
- Metabolic diversification of nitrogen‐containing metabolites by expression of a heterologous lysine decarboxylase gene in Arabidopsis
- (2019) Yohei Shimizu et al. PLANT JOURNAL
- Modern technologies and algorithms for scaffolding assembled genomes
- (2019) Jay Ghurye et al. PLoS Computational Biology
- Transcription Factor OpWRKY3 Is Involved in the Development and Biosynthesis of Camptothecin and Its Precursors in Ophiorrhiza pumila Hairy Roots
- (2019) Can Wang et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Variations in common diseases, hospital admissions, and deaths in middle-aged adults in 21 countries from five continents (PURE): a prospective cohort study
- (2019) Gilles R Dagenais et al. LANCET
- Present status of Catharanthus roseus monoterpenoid indole alkaloids engineering in homo- and hetero-logous systems
- (2019) Abhishek Sharma et al. BIOTECHNOLOGY LETTERS
- Parallelization of MAFFT for large-scale multiple sequence alignments
- (2018) Tsukasa Nakamura et al. BIOINFORMATICS
- Metabolomics fingerprint of coffee species determined by untargeted-profiling study using LC-HRMS
- (2018) Florence Souard et al. FOOD CHEMISTRY
- Plant Secondary Metabolites as Anticancer Agents: Successes in Clinical Trials and Therapeutic Application
- (2018) Ana Seca et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Use of a draft genome of coffee (Coffea arabica ) to identify SNPs associated with caffeine content
- (2018) Hue T.M. Tran et al. PLANT BIOTECHNOLOGY JOURNAL
- Solution of the multistep pathway for assembly of corynanthean, strychnos, iboga, and aspidosperma monoterpenoid indole alkaloids from 19E-geissoschizine
- (2018) Yang Qu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data
- (2018) Rubina Jibran et al. Horticulture Research
- The opium poppy genome and morphinan production
- (2018) Li Guo et al. SCIENCE
- Gene Discovery in Gelsemium Highlights Conserved Gene Clusters in Monoterpene Indole Alkaloid Biosynthesis
- (2018) Jakob Franke et al. CHEMBIOCHEM
- Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation
- (2017) Sergey Koren et al. GENOME RESEARCH
- TimeTree: A Resource for Timelines, Timetrees, and Divergence Times
- (2017) Sudhir Kumar et al. MOLECULAR BIOLOGY AND EVOLUTION
- BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
- (2017) Robert M Waterhouse et al. MOLECULAR BIOLOGY AND EVOLUTION
- The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution
- (2017) Hélène Badouin et al. NATURE
- Reconstructing the genome of the most recent common ancestor of flowering plants
- (2017) Florent Murat et al. NATURE GENETICS
- Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
- (2017) Derek M Bickhart et al. NATURE GENETICS
- plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters
- (2017) Satria A. Kautsar et al. NUCLEIC ACIDS RESEARCH
- The MetaCyc database of metabolic pathways and enzymes
- (2017) Ron Caspi et al. NUCLEIC ACIDS RESEARCH
- Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
- (2017) Ioanna Kalvari et al. NUCLEIC ACIDS RESEARCH
- A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants
- (2017) Jennifer H. Wisecaver et al. PLANT CELL
- Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants
- (2017) Pascal Schläpfer et al. PLANT PHYSIOLOGY
- Taxonomic structure and functional association of foxtail millet root microbiome
- (2017) Tao Jin et al. GigaScience
- Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software
- (2016) Hiroshi Tsugawa et al. ANALYTICAL CHEMISTRY
- ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
- (2016) Jaime Huerta-Cepas et al. MOLECULAR BIOLOGY AND EVOLUTION
- Phased diploid genome assembly with single-molecule real-time sequencing
- (2016) Chen-Shan Chin et al. NATURE METHODS
- Plant metabolic clusters - from genetics to genomics
- (2016) Hans-Wilhelm Nützmann et al. NEW PHYTOLOGIST
- PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants
- (2016) Jinpu Jin et al. NUCLEIC ACIDS RESEARCH
- An MYB transcription factor regulating specialized metabolisms in Ophiorrhiza pumila
- (2016) Emelda Rosseleena Rohani et al. Plant Biotechnology
- A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution
- (2016) James K. Hane et al. PLANT BIOTECHNOLOGY JOURNAL
- Metabolite Diversity in Alkaloid Biosynthesis: A Multilane (Diastereomer) Highway for Camptothecin Synthesis in Camptotheca acuminata
- (2016) Radin Sadre et al. PLANT CELL
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- (2016) Candice N. Hirsch et al. PLANT CELL
- Draft genome assembly and annotation of Glycyrrhiza uralensis , a medicinal legume
- (2016) Keiichi Mochida et al. PLANT JOURNAL
- Evolution of gene duplication in plants
- (2016) Nicholas Panchy et al. PLANT PHYSIOLOGY
- Function of AP2/ERF Transcription Factors Involved in the Regulation of Specialized Metabolism in Ophiorrhiza pumila Revealed by Transcriptomics and Metabolomics
- (2016) Nirin Udomsom et al. Frontiers in Plant Science
- Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
- (2016) Neva C. Durand et al. Cell Systems
- The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae
- (2016) Jamal S. M. Sabir et al. Scientific Reports
- Gene-Wide Identification of Episodic Selection
- (2015) Ben Murrell et al. MOLECULAR BIOLOGY AND EVOLUTION
- Monoterpenoid indole alkaloids biosynthesis and its regulation in Catharanthus roseus: a literature review from genes to metabolites
- (2015) Qifang Pan et al. PHYTOCHEMISTRY REVIEWS
- Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement
- (2015) Jose J. De Vega et al. Scientific Reports
- Repbase Update, a database of repetitive elements in eukaryotic genomes
- (2015) Weidong Bao et al. Mobile DNA
- HTSeq--a Python framework to work with high-throughput sequencing data
- (2014) S. Anders et al. BIOINFORMATICS
- Trimmomatic: a flexible trimmer for Illumina sequence data
- (2014) Anthony M. Bolger et al. BIOINFORMATICS
- InterProScan 5: genome-scale protein function classification
- (2014) P. Jones et al. BIOINFORMATICS
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication
- (2014) G Albert Wu et al. NATURE BIOTECHNOLOGY
- Single-copy gene-based chromosome painting in cucumber and its application for chromosome rearrangement analysis inCucumis
- (2014) Qunfeng Lou et al. PLANT JOURNAL
- Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
- (2014) Bruce J. Walker et al. PLoS One
- Genomic Signatures of Specialized Metabolism in Plants
- (2014) L. Chae et al. SCIENCE
- The coffee genome provides insight into the convergent evolution of caffeine biosynthesis
- (2014) F. Denoeud et al. SCIENCE
- The seco-iridoid pathway from Catharanthus roseus
- (2014) Karel Miettinen et al. Nature Communications
- Informed and automated k-mer size selection for genome assembly
- (2013) R. Chikhi et al. BIOINFORMATICS
- Infernal 1.1: 100-fold faster RNA homology searches
- (2013) E. P. Nawrocki et al. BIOINFORMATICS
- Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement
- (2013) Rajeev K Varshney et al. NATURE BIOTECHNOLOGY
- Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
- (2013) Joshua N Burton et al. NATURE BIOTECHNOLOGY
- The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
- (2013) Ignazio Verde et al. NATURE GENETICS
- De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
- (2013) Brian J Haas et al. Nature Protocols
- Coupling Deep Transcriptome Analysis with Untargeted Metabolic Profiling in Ophiorrhiza pumila to Further the Understanding of the Biosynthesis of the Anti-Cancer Alkaloid Camptothecin and Anthraquinones
- (2013) Mami Yamazaki et al. PLANT AND CELL PHYSIOLOGY
- MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations
- (2013) M. S. Campbell et al. PLANT PHYSIOLOGY
- Genomic rearrangements and the evolution of clusters of locally adaptive loci
- (2013) S. Yeaman PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes
- (2013) M. Itkin et al. SCIENCE
- The Amborella Genome and the Evolution of Flowering Plants
- (2013) et al. SCIENCE
- The Banana Genome Hub
- (2013) Gaëtan Droc et al. Database-The Journal of Biological Databases and Curation
- Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)
- (2013) Ray Ming et al. GENOME BIOLOGY
- CD-HIT: accelerated for clustering the next-generation sequencing data
- (2012) Limin Fu et al. BIOINFORMATICS
- Evolutionary Dynamics and Functional Specialization of Plant Paralogs Formed by Whole and Small-Scale Genome Duplications
- (2012) Lorenzo Carretero-Paulet et al. MOLECULAR BIOLOGY AND EVOLUTION
- A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research
- (2012) Aureliano Bombarely et al. MOLECULAR PLANT-MICROBE INTERACTIONS
- Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
- (2012) Andrew H. Paterson et al. NATURE
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
- (2012) Cole Trapnell et al. Nature Protocols
- MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
- (2012) Y. Wang et al. NUCLEIC ACIDS RESEARCH
- Suppression of camptothecin biosynthetic genes results in metabolic modification of secondary products in hairy roots of Ophiorrhiza pumila
- (2012) Takashi Asano et al. PHYTOCHEMISTRY
- Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
- (2012) Adam C. English et al. PLoS One
- The Pathway Tools Pathway Prediction Algorithm
- (2012) Peter D. Karp et al. Standards in Genomic Sciences
- A genome triplication associated with early diversification of the core eudicots
- (2012) Yuannian Jiao et al. GENOME BIOLOGY
- Adaptive seeds tame genomic sequence comparison
- (2011) S. M. Kielbasa et al. GENOME RESEARCH
- The Medicago genome provides insight into the evolution of rhizobial symbioses
- (2011) Nevin D. Young et al. NATURE
- Full-length transcriptome assembly from RNA-Seq data without a reference genome
- (2011) Manfred G Grabherr et al. NATURE BIOTECHNOLOGY
- The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
- (2011) Philippe Lamesch et al. NUCLEIC ACIDS RESEARCH
- The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants
- (2011) Rafał Wóycicki et al. PLoS One
- The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants
- (2011) J. A. Banks et al. SCIENCE
- Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood
- (2010) M. Csuos BIOINFORMATICS
- Genome sequence of the palaeopolyploid soybean
- (2010) Jeremy Schmutz et al. NATURE
- The genome of the domesticated apple (Malus × domestica Borkh.)
- (2010) Riccardo Velasco et al. NATURE GENETICS
- The Gypsy Database (GyDB) of mobile genetic elements: release 2.0
- (2010) C. Llorens et al. NUCLEIC ACIDS RESEARCH
- Correlation of Camptothecin-producing Ability and Phylogenetic Relationship in the GenusOphiorrhiza
- (2010) Varalee Viraporn et al. PLANTA MEDICA
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- Using native and syntenically mapped cDNA alignments to improve de novo gene finding
- (2008) Mario Stanke et al. BIOINFORMATICS
- Mutations in topoisomerase I as a self-resistance mechanism coevolved with the production of the anticancer alkaloid camptothecin in plants
- (2008) S. Sirikantaramas et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Plant-derived compounds in clinical trials
- (2007) A SAKLANI et al. DRUG DISCOVERY TODAY
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